Modela-r as a Froude and Strouhal dimensionless numbers combination for dynamic similarity in running

The aim of this study was to test the hypothesis that running at fixed fractions of Froude (Nfr) and Strouhal (Str) dimensionless numbers combinations induce dynamic similarity between humans of different sizes. Nineteen subjects ran in three experimental conditions, (i) constant speed, (ii) similar speed (Nfr) and (iii) similar speed and similar step frequency (Nfr and Str combination). In addition to anthropometric data, temporal, kinematic and kinetic parameters were assessed at each stage to measure dynamic similarity informed by dimensional scale factors and by the decrease of dimensionless mechanical parameter variability. Over a total of 54 dynamic parameters, dynamic similarity from scale factors was met for 16 (mean r=0.51), 32 (mean r=0.49) and 52 (mean r=0.60) parameters in the first, the second and the third experimental conditions, respectively. The variability of the dimensionless preceding parameters was lower in the third condition than in the others. This study shows that the combination of Nfr and Str, computed from the dimensionless energy ratio at the center of gravity (Modela-r) ensures dynamic similarity between different-sized subjects. The relevance of using similar experimental conditions to compare mechanical dimensionless parameters is also proved and will highlight the study of running techniques, or equipment, and will allow the identification of abnormal and pathogenic running patterns. Modela-r may be adapted to study other abilities requiring bounces in human or animal locomotion or to conduct investigations in comparative biomechanics.     

Investigation of transmitter-receptor interactions by analyzing postsynaptic membrane noise using stochastic kinetics

The stoichiometric and kinetic details of transmitter-receptor interaction (the number of conformations and the rate constants of conformation changes) in synaptic transmission have been investigated analyzing postsynaptic membrane noises by the aid of the fluctuation-dissipation theorem of stochastic chemical kinetics. The main assumptions are the following: (i) the transmitter-receptor interaction is modelled by a closed compartment system (a special complex chemical reaction) of unknown length,- (ii) the quantity of transmitter is maintained at a constant level,- (iii) the conductance is a linear function of the conformation quantity vector.- The main conclusion is: the conductance spectral density function is determined by three qualitatively different factors: (i) the length of the compartment system,- (ii) the precise form of the conductance-conformation quantity vector,-(iii) the matrix of the reaction rate constants.     

Temperature distribution in human skin and subdermal tissues

Temperature profiles have been computed in the skin and subdermal part of a human body for (i) various values of environmental temperature, rate of sweat evaporation and wind velocity, (ii) rate of blood mass flow, (iii) rate of metabolic heat generation and (iv) three different sets of thicknesses of skin layers. The mathematical equations have been considered for a one-dimensional steady-state case. The two important physical parameters, namely rate of blood mass flow and rate of metabolic heat generation, have been assigned position-dependent values. The latter is also taken as linearly dependent on the tissue temperature. Analytic solutions have been obtained for the three layers of the region. These forms of solution facilitate the study of parameter dependence.     

A two-phase model for flow of blood in narrow tubes with increased effective viscosity near the wall

A two-phase model for the flow of blood in narrow tubes is described. The model consists of a central core of suspended erythrocytes and a cell-free layer surrounding the core. It is assumed that the viscosity in the cell-free layer differs from that of plasma as a result of additional dissipation of energy near the wall caused by the red blood cell motion near the cell-free layer. A consistent system of nonlinear equations is solved numerically to estimate: (i) the effective dimensionless viscosity in the cell-free layer (beta), (ii) thickness of the cell-free layer (1-lambda) and (iii) core hematocrit (H(c)). We have taken the variation of apparent viscosity (mu(app)) and tube hematocrit with the tube diameter (D) and the discharge hematocrit (H(D)) from in vitro experimental studies [16]. The thickness of the cell-free layer computed from the model is found to be in agreement with the observations [3,21]. Sensitivity analysis has been carried out to study the behavior of the parameters 1-lambda, beta, H(c), B (bluntness of the velocity profile) and mu(app) with the variation of D and H(D).     

Electrostatic plasma turbulence and spitzer longitudinal conductivity in tokamaks

An analysis has revealed that there may be three radically different steady states of a tokamak plasma: (i) discharges in which the electron and ion transport can be described by neoclassical theory; (ii) discharges with the Spitzer longitudinal conductivity, neoclassical ion transport, and “anomalous” electron transport; and (iii) discharges in which the electron transport and ion transport are both “anomalous.” The dimensionless parameters responsible for the occurrence of the three types of discharges are determined. In accordance with the criteria derived for the achievement of different steady states, discharges of the second type are most typical of modern tokamaks and discharges of the third type can occur only if the turbulence is sufficiently strong. Discharges of the first type cannot occur in the range of the working parameters of present-day tokamaks and future tokamak reactors, but they can be ignited in a large class of magnetic confinement systems. The physical reason for the onset of different types of discharges is associated with the fact that turbulent fluctuations play very different roles in the dynamics of the ion and electron components of a finite-size magnetized plasma. The question of the self-consistency between the profiles is considered. A law is derived according to which the thermal diffusivity increases toward the plasma edge.     

Restriction mapping of synthetic thyroglobulin structural gene as a means of investigating thyroglobulin structure

Bovine 33 S thyroglobulin mRNA was reverse transcribed into double-stranded DNA under conditions allowing the synthesis of a complete 8 kilobase pair copy. A physical map of the resulting synthetic thyroglobulin structural gene was constructed using six restriction endonucleases. The following conclusions could be drawn: (i) the polypeptide chains in thyroglobulin subunits are identical; (ii) thyroglobulin is composed of a major class of molecules sharing the same primary structure; (iii) there is no evidence for precise internal repetition in the structure of thyroglobulin subunits.     

Analytical solutions to the multicylinder somatic shunt cable model for passive neurones with differing dendritic electrical parameters

The multicylinder somatic shunt cable model for passive neurones with differing time constants in each cylinder is considered in this paper. The solution to the model with general inputs is developed, and the parametric dependence of the voltage response is investigated. The method of analysis is straightforward and follows that laid out in Evans et al. (1992, 1994): (i) The dimensional problem is stated with general boundary and initial conditions, (ii) The model is fully non-dimensionalised, and a dimensionless parameter family which uniquely governs the behaviour of the dimensionless voltage response is obtained, (iii) The fundamental unit impulse problem is solved, and the solutions to problems involving general inputs are written in terms of the unit impulse solution, (iv) The large and small time behaviour of the unit impulse solution is examined, (v) The parametric dependence of the unit impulse upon the dimensionless parameter family is explored for two limits of practical interest. A simple expression for the principle relationship between the dimensionless parameter family is derived and provides insight into the interaction between soma and cylinders. A well-posed method for the solution of the dimensional inverse problem is presented.     

Dimensional analysis in mathematical biology. II

The application of dimensional analysis in biology is further illustrated by functional equations composed of dimensionless numbers and dealing with renal physiology, lung physiology and plant leaf shape. Dimensional variables and dimensionless numbers are examined from the viewpoint of numerical invariant properties of a certain physical system. Utilization of the method for problems such as design of an artificial kidney is considered briefly. A tabulation of variables useful in biology is given, with suggestions for a number of new dimensional entities. A continuation of the list of dimensionless invariants from Part I (Bull. Math. Biophysics,23, 355–376, 1961) is provided and includes terms pertaining to general physiology, geometric growth, metabolism, ecological interactions, muscle kinetics and other areas. It is pointed out that use of dimensionless ratios (similarity criteria) makes possible a direct comparison of form or shape factors and relative growth ratios with a variety of physical ratios, through the use of functional equations containing only dimensionless entities. Organismal similarity during growth and development, and between genetically related species, may be analyzed in terms of “automodel” or “self-similar” systems governed by certain dimensionless invariants. Tables of biological variables and dimensionless groupings are included.     

Enzyme organization and stability of metabolic pathways: A comparison of various approaches

The aim of this paper is to compare various methods for the quantification of metabolic pathways dynamics. A Yates-Pardee metabolic pathway with enzyme organization, i.e. with spatial localization of the enzymes in a specific cellular compartment, was studied using: (i) the classical Henri-Michaelis-Menten (HMM) equations, (ii) linearization of the HMM equations in the vicinity of a steady state (linearized formalism), and (iii) Biochemical Systems Theory formalism (BST formalism). It is shown that transient solutions computed via either the linearized formalism or the BST formalism can greatly differ from transient solutions computed with the HMM equations. However, in the studied example, results remain qualitatively the same for the three formalisms. This suggests that the study of the topology of the system may give useful insights into the metabolic pathways dynamics.     

Effects of phosphate buffer capacity of soil on the phosphate requirements of plants

Summary Plant-uptake and yield data for ryegrass in a greenhouse experiment are used to estimate the theoretical fertilizer phosphate requirement (Pf) of 24 Sherborne soils. Pf is shown to be a function of three parameters: (i) quantity of P required by the plant (Pr) for optimum yield; (ii) quantity of soil P (Qr) required to maintain a non-limiting soil solution concentration (Ir); (iii) quantity of labile soil P (Q). Because of its large effect on Qr and Ir, the phosphate buffer capacity has an important effect on Pf. However Pf cannot be directly related to phosphate buffer capacity if Q is ignored. On soils of similar Q, increasing buffer capacity will always have a positive effect on Pf, but on soils of the same I, it may have a positive or negative effect on Pf. Consequently, Pf can only be simply, but inversely, related to Q or I on a group of soils of similar phosphate buffer capacity. re]19750513     

Estimation of viable airborne microbes downwind from a point source.

Modification of the Pasquill atmospheric diffusion equations for estimating viable microbial airborne cell concentrations downwind form a continuous point source is presented. A graphical method is given to estimate the ground level cell concentration given (i) microbial death rate, (ii) mean wind speed, (iii) atmospheric stability class, (iv) downwind sample distance from the source, and (v) source height.     

Differential cDNA cloning by enzymatic degrading subtraction (EDS).

We describe a new method, called enzymatic degrading subtraction (EDS), for the construction of subtractive libraries from PCR amplified cDNA. The novel features of this method are that i) the tester DNA is blocked by thionucleotide incorporation; ii) the rate of hybridization is accelerated by phenol-emulsion reassociation; and iii) the driver cDNA and hybrid molecules are enzymatically removed by digestion with exonucleases III and VII rather than by physical partitioning. We demonstrate the utility of EDS by constructing a subtractive library enriched for cDNAs expressed in adult but not in embryonic rat brains.     

Double Diffusive Magnetohydrodynamic (MHD) Mixed Convective Slip Flow along a Radiating Moving Vertical Flat Plate with Convective Boundary Condition

In this study combined heat and mass transfer by mixed convective flow along a moving vertical flat plate with hydrodynamic slip and thermal convective boundary condition is investigated. Using similarity variables, the governing nonlinear partial differential equations are converted into a system of coupled nonlinear ordinary differential equations. The transformed equations are then solved using a semi-numerical/analytical method called the differential transform method and results are compared with numerical results. Close agreement is found between the present method and the numerical method. Effects of the controlling parameters, including convective heat transfer, magnetic field, buoyancy ratio, hydrodynamic slip, mixed convective, Prandtl number and Schmidt number are investigated on the dimensionless velocity, temperature and concentration profiles. In addition effects of different parameters on the skin friction factor, , local Nusselt number, , and local Sherwood number are shown and explained through tables.     

Dynamic similarity during human running: About Froude and Strouhal dimensionless numbers

Dynamic similarity is a widely used concept in the fluid mechanics field, and consists in placing two different-sized systems in equivalent experimental conditions. This enables removal of the effects of size and prediction of the behavior of a full size system from a scale model. The aim of this study was to test whether the Froude number (Nfr) or the Strouhal number (Str) could be used as a criterion for dynamic similarity during running. Fifteen male subjects ran barefoot on a runway in three experimental conditions (i) all subjects ran at the same speed V=3.5 m s^?1; (ii) the speed was determined from Nfr; (iii) the stride frequency was determined from Str. Antero-posterior (Fy) and vertical (Fz) ground reaction force components were assessed. The similarity between the subjects was analysed from scale factor sets computed from anthropometric and kinetic data. The use of Str implied strong inter-subject similarity for temporal parameters (mean r=0.96, time to Fz peak, time to Fy braking peak, Fy zero fore–aft shear, time to Fy propulsive peak) while Nfr induced fewer and lower similarities (mean r=0.75, Fy zero fore–aft shear, time to Fy propulsive peak, Fy braking impulse) that only concerned antero-posterior parameters. This study brought experimental evidence that neither Nfr nor Str were sufficient for dynamic similarity during running, but that each of them made its own contribution. These findings suggested that the concomitant use of Nfr and Str should be assessed to induce inter-subject dynamic similarity during running.     

A strategy for finding regions of similarity in complete genome sequences

MOTIVATION: Complete genomic sequences will become available in the future. New methods to deal with very large sequences (sizes beyond 100 kb) efficiently are required. One of the main aims of such work is to increase our understanding of genome organization and evolution. This requires studies of the locations of regions of similarity. RESULTS: We present here a new tool, ASSIRC ('Accelerated Search for SImilarity Regions in Chromosomes'), for finding regions of similarity in genomic sequences. The method involves three steps: (i) identification of short exact chains of fixed size, called 'seeds', common to both sequences, using hashing functions; (ii) extension of these seeds into putative regions of similarity by a 'random walk' procedure; (iii) final selection of regions of similarity by assessing alignments of the putative sequences. We used simulations to estimate the proportion of regions of similarity not detected for particular region sizes, base identity proportions and seed sizes. This approach can be tailored to the user's specifications. We looked for regions of similarity between two yeast chromosomes (V and IX). The efficiency of the approach was compared to those of conventional programs BLAST and FASTA, by assessing CPU time required and the regions of similarity found for the same data set. AVAILABILITY: Source programs are freely available at the following address: ftp://ftp.biologie.ens. fr/pub/molbio/assirc.tar.gz CONTACT: vincens@biologie.ens.fr, hazout@urbb.jussieu.fr      

New expressions to describe solution nonideal osmotic pressure, freezing point depression, and vapor pressure.

New empirical expressions for osmotic pressure, freezing point depression, and vapor pressure are proposed based on the concepts of volume occupancy and (or) hydration force. These expressions are in general inverse relationships in comparison to the standard ideal expressions for the same properties. The slopes of the new equations are determined by the molecular weight of the solute and known constants. The accuracy and precision of the molecular weights calculated from the slope are identical and approximately 1% for the experiments reported here. The nonideality of all three colligative expressions is described by a dimensionless constant called the solute-solvent interaction parameter I. The results on sucrose have the same I = 0.26 for all three solution properties. The nonideality parameter I increased from 0.26 on sucrose to 1.7 on hemoglobin to successfully describe the well-known nonideal response of macromolecules.     

A conserved BURP domain defines a novel group of plant proteins with unusual primary structures

We have identified a new class of plant proteins containing a common C-terminal region, which we have termed the BURP domain. These proteins are defined not only by the BURP domain, but also by the overall similarity in their modular construction. The BURP domain proteins consist of either three or four modules: (i) an N-terminal hydrophobic domain – a presumptive transit peptide, joined to (ii) a short conserved segment or other short segment, (iii) an optional segment consisting of repeated units which is unique to each member, and (iv) the C-terminal BURP domain. These individual modules appear to be combined to form two main classes of BURP domain proteins. The BURP domain proteins, despite the similarities in their primary structural features, show no obvious similarities in the tissues or conditions under which they are expressed. The presence of the conserved BURP domain in diverse plant proteins suggests an important and fundamental functional role for this domain. Received: 30 April 1998 / Accepted: 10 June 1998     

The role of His-50 of α-synuclein in binding Cu(II): pH dependence, speciation, thermodynamics and structure

Copper interaction with alpha synuclein (αS) has been shown to accelerate aggregation and oligomerization of the protein. Three different αS copper binding domains have been proposed: (i) the N-terminal residues (1-9) that represent the minimal copper binding domain; (ii) the His-50 imidazole and (iii) the Asp and Glu residues within the acidic C-terminal domain. The copper coordination at the N-terminus has been extensively characterized and it is generally accepted that it provides the highest affinity site. The same does not hold for the role played by His-50 in copper binding. In this work Cu(ii) coordination to peptide fragments encompassing residues 45-55 of αS has been exhaustively characterized, including systems containing the inherited mutations E46K and A53T, as model peptides of the His-50 site. Through potentiometric titrations all the speciation profiles have been determined and the stability constants have been used to estimate the dissociation constants of complexes corresponding to the binding modes at pH 6.5 and 7.5. Spectroscopic analyses allowed determination of (i) the copper coordination sphere, (ii) its geometry and (iii) the constraints wherefrom the 3D structural models of the copper complexes could be obtained.     

Identification of Nsp100 as elongation factor 2 (EF-2)

The nerve growth factor-sensitive phosphoprotein from PC12 cells, previously designated Nsp100, has been shown to be elongation factor 2 (EF-2). The criteria used for this identification include: (i) similarity of N-terminal sequence; (ii) phosphorylation by the same kinase; (iii) ADP-ribosylation mediated by diphtheria toxin; (iv) comparable function in cell-free protein synthesis. According to these criteria, Nsp100 and EF-2 are identical and the kinase that phosphorylates Nsp100 in PC12 cells is calcium/calmodulin kinase III.     

Amino acidic scaffolds bearing unnatural side chains: An old idea generates new and versatile tools for the life sciences

The unnatural amino acids (UAAs) are members of a class of molecules with relevant impacts in the life sciences. Due to the role of these molecules in the modulation of the chemical and physical properties of biological and inorganic materials, UAAs have attracted increasing interest in recent years. The aim of this review is to highlight (i) the most recent and innovative synthetic routes for the preparation of UAAs, (ii) the recently marketed UAA-based drugs, and (iii) the most promising technological applications involving novel UAA-containing molecular entities.